We now know that there are molecular machines within living cells that take useless blobs of misfolded proteins and untangle them. They then refold them so that they may serve their proper function in the cell. In like manner, my computer printer has certain routines it can run to clean dirty print heads and perform other similar routine maintenance tasks. The living cell has far more sophisticated repair mechanisms than any machines humans have constructed. This is an indication that the cell is a very well designed system.
In human cells useless blobs of misfolded proteins may be part of the problem that is expressed as diseases such as Alzheimer's and Parkinson's. The journal Science reports on recent advances in protein folding research, but labels these cellular capabilities a "remarkable" case of "evolved machinery":
Protein misfolding and aggregation would drastically shorten the life of cells were it not for the molecular chaperones that prevent these damaging processes. In vitro, aggregation is irreversible under physiological conditions. Remarkably, the cells of bacteria, plants, and fungi have evolved machinery to neatly extract polypeptide chains from large aggregates and refold them to the native state, with little specificity for protein sequence or fold.
ENV offers this comment about the article in Nature.
What this means is that lab technicians can't untangle these blobs in a petri dish, but cells manage to do it. It is remarkable indeed that cells have "evolved" machinery to do what humans cannot. The phrase "with little specificity" indicates that the machinery is general-purpose: it can take most any clump and untangle it.... We don't need to get into the details of machine parts and their names. The author of the Science article, biologist Helen R. Saibil, provides a model diagram of this "highly dynamic" machine and descriptions of what the parts do. There are channels, toggles, linkers, mobile lids, and dockers. One of the primary parts looks like a stack of 3-tiered rings with a channel down the middle. The other part looks a little like Pac-man, biting down on a "hot spot" on the side of the rings, accompanied by other moving parts. Each of the primary parts is further composed of several protein domains. Multiple ATP "energy pellets" power the operation at three locations.
Later this ENV article notes:
Nothing about this looks Darwinian. It's another case of irreducible complexity: machinery with multiple interacting parts, each necessary for function. The machinery is already there in the simplest cells. It's essential for cells to survive. It certainly looks designed.
Maybe that's why Helen Saibil says so little about evolution, other than her comment that "Remarkably, the cells of bacteria, plants, and fungi have evolved machinery to neatly extract polypeptide chains from large aggregates and refold them." In that sentence, the word "evolved" functions only as a distraction, not as a guide to understanding anything.
In another ENV article, "Nothing about Molecular Machines Makes Sense without Intelligent Design," we learn about another related topic: The cellular highway system. A number of little machines makes this possible within the living cell.
Cells use molecular vehicles that carry cargo on networks of "highways." Some scientists can't avoid the comparison to modern vehicular traffic. Brookhaven National Laboratory reports:
Molecular motor proteins inside the body, called kinesins, are a lot like the motor in your car. The molecular motors convert stored chemical energy into specific conformational changes, which lead to various movements in cells, analogous to the way a car engine converts the energy of gasoline combustion into torque generation, which leads to tires rotating on an axle.
The analogy proceeds seamlessly into a discussion of how Dartmouth College researchers have succeeded in tweaking the kinesin motor by adding a "switch" to "to control the activity of these organic nanomotors." Kinesins don't come with an "ignition switch," so the researchers exchanged a magnesium atom for manganese, giving them the ability to stop and start the kinesin engine:"Now we have the ability to tightly control the speed of these motors, such that we can 'turn them off' and 'turn them back on' similar to a dimmer switch on your lights at home," said Jared Cochran, who worked with a team to devise the control "switch" for kinesin motors. They found that in the presence of magnesium, the engineered enzyme stops functioning. But introduce manganese, and it will jumpstart the motor protein again.
Read more of this aritcle here.